Methods for systemically delivering polypeptides and microorganisms therefor

ABSTRACT

Methods and microorganisms for systemically introducing a polypeptide in the bloodstream of a subject. The methods of the invention include administering into the gastrointestinal tract of a subject a bacterium configured to express and produce and release the polypeptide. The bacterium is administered in an amount effective to introduce the polypeptide in the bloodstream of the subject, preferably in a detectable amount. The microorganisms of the invention include lactic acid bacteria, such as  Lactobacillus reuteri , that comprise a recombinant gene configured to express a polypeptide to be systemically introduced.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under DK101573 andDK102948 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

FIELD OF THE INVENTION

The invention is directed to systemically delivering polypeptides to thebloodstream of a subject, such as through administering into thegastrointestinal tract of the subject a microorganism that produces andreleases the polypeptides. The invention is also directed tomicroorganisms suitable for this purpose.

BACKGROUND

Polypeptides, such as enzymes, antibodies, hormones, cytokines, etc.,are tremendously useful as therapeutic agents. However, routes forsystemically introducing such polypeptides to a subject are limited.Oral administration of the polypeptides is typically not feasible, asthe polypeptides are either degraded in the gastrointestinal tract orare blocked from reaching the bloodstream. Direct intravenousadministration is therefore the major route by which polypeptides aresystemically introduced.

Certain types of genetically engineered bacteria have been used asvehicles for locally delivering polypeptides to various tissues.Engineered Lactococcus lactis, for example, has been administeredintragastrically for delivering polypeptides such as trefoil factors andinterleukin-10 locally to intestinal/mucosal tissues. See Steidler etal. 2000 and Huyghebaert et al. 2005. However, a systemic increase inpolypeptides delivered via Lactococcus lactis was not found.

Other types of genetically engineered bacteria have been used asvehicles for delivery of polypeptides to tumors in the body. Anengineered Bifidobacterium strain, for example, has been shown totranslocate from the gastrointestinal tract after oral administrationand target to, replicate in, and express genes within tumors. See Croninet al. 2010. This effect, however, depends on the unique ability of theBifidobacterium to translocate from the gastrointestinal tract toextra-intestinal sites in the body. While Bifidobacterium may serve as auseful delivery vehicle for some purposes, the systemic distribution ofthe Bifidobacterium is potentially deleterious in certain subjectpopulations such as immunocompromised patients.

Engineered bacteria capable of being administering into thegastrointestinal tract and delivering polypeptides in the bloodstreamwithout systemic levels of the bacteria themselves being increased areneeded.

SUMMARY OF THE INVENTION

The invention is directed to methods and microorganisms for systemicallyintroducing a polypeptide in a bloodstream of a subject.

One method comprises administering into the gastrointestinal tract ofthe subject a bacterium configured to produce and release thepolypeptide. The bacterium may comprise a recombinant gene configured toexpress the polypeptide. The bacterium is administered in an amounteffective to introduce the polypeptide in the bloodstream of thesubject, preferably in a detectable amount.

In some versions, the bacterium is administered in an amount effectiveto introduce the polypeptide in the bloodstream of the subject withoutthe bacterium being substantially introduced in the bloodstream of thesubject.

In some versions, the bacterium is administered in an amount effectiveto introduce the polypeptide in the bloodstream in an amount effectiveto induce at least one direct systemic effect in the subject. In someversions, the bacterium is administered in an amount effective tointroduce the polypeptide in the bloodstream in an amount effective toinduce at least one direct effect in a non-gastrointestinal tissue inthe subject. In some versions, the bacterium is administered in anamount effective to introduce the polypeptide in the bloodstream in anamount effective to induce at least one direct effect in a tissueselected from the group consisting of liver, muscles, lungs, kidneys,pancreas, and adipose tissue in the subject.

In some versions, the subject suffers from a condition treatable withsystemic introduction of the polypeptide. In some versions, the subjectsuffers from a condition treatable with systemic introduction of thepolypeptide but not treatable with local introduction of the polypeptideto the gastrointestinal tract without systemic introduction of thepolypeptide. In either case, the polypeptide is introduced in thebloodstream of the subject in an amount effective to treat thecondition, independent of the bacterium getting into the bloodstream.

In some versions, the polypeptide is a therapeutic polypeptide.

In some versions, the polypeptide is selected from the group consistingof a cytokine, a hormone, an antibody, an antimicrobial peptide, and anantigenic peptide.

In some versions, the polypeptide is selected form the group consistingof IL-22, IL-35, insulin, leptin, cathelicidin related antimicrobialpeptide, a peptide inhibitor of PCSK9, and an endolysin.

In some versions, the subject suffers from at least one conditionselected from the group consisting of insulin resistance, hyperglycemia,lipid dysregulation, hyperlipidemia, and obesity, and wherein thepolypeptide is introduced in the bloodstream of the subject in an amounteffective to treat the at least one condition.

In some versions, the bacterium comprises a bacterium other than amember of the Bifidobacterium genus. In some versions, the bacteriumcomprises a member of lactic acid bacteria, such as a member of lacticacid bacteria other than a member of the Lactococcus genus. In someversions, the bacterium comprises a member of Lactobacillus, such asLactobacillus reuteri.

A microorganism of the invention comprises a bacterium comprising arecombinant gene configured to express a polypeptide, wherein thebacterium is configured to produce and release the polypeptide and iscapable of introducing the polypeptide in the bloodstream of thesubject.

In some versions, the bacterium is capable of introducing thepolypeptide in the bloodstream of the subject without the bacteriumbeing substantially introduced in the bloodstream of the subject.

In some versions, the polypeptide is capable of treating a condition ina subject with systemic introduction of the polypeptide in the subject.

In some versions, the polypeptide is selected form the group consistingof IL-22, IL-35, insulin, leptin, cathelicidin related antimicrobialpeptide, a peptide inhibitor of PCSK9, and an endolysin.

In some versions, the bacterium comprises a bacterium other than amember of the Bifidobacterium genus. In some versions, the bacteriumcomprises a member of lactic acid bacteria, such as a member of lacticacid bacteria other than a member of the Lactococcus genus. In someversions, the bacterium comprises a member of Lactobacillus, such asLactobacillus reuteri.

The objects and advantages of the invention will appear more fully fromthe following detailed description of the preferred embodiment of theinvention made in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B show mutation rates of various types of bacteria.

FIG. 2 is a plasmid map of the pVPL3461 murine interleukin-22(mIL-22)-expressing plasmid of the invention, showing an erythromycinresistance gene (Em), an chloramphenicol resistance gene coding sequence(Cm), a phelp promoter (Phelp) (Riedel et al. 2007) for thechloramphenicol resistance gene coding sequence, an mIL-22 codingsequence (mIL-22), a signal peptide for secretion of mIL-22 (SP), apromoter for the signal peptide and the mIL-22 coding sequence(Promoter), and an inverted repeat (IR), which serves as atranscriptional terminator.

FIGS. 3A and 3B show secretion of mIL-22 from engineered L. reutericells. FIG. 3A shows mIL-22 secretion from L. reuteri cells harboringthe pVPL3461 plasmid compared to wild-type L. reuteri cells as acontrol. FIG. 3B shows mIL-22 secretion from L. reuteri cells harboringa chromosomal copy of a mIL-22 gene compared to wild-type L. reutericells as a control.

FIG. 4 shows a schema of methods for assessing delivery of mIL-22 tomice from orally administered L. reuteri cells harboring the pVPL3461plasmid, including detecting plasma mIL-22 levels and determiningexpression of mIL-22 target genes reg3-beta and reg3-gamma.

FIG. 5 shows plasma IL-22 levels in sham gavaged mice (untreated), micegavaged with wild-type L. reuteri (1×10⁹ CFU), and mice gavaged with L.reuteri engineered to secrete IL-22 (1×10⁹ CFU). Eight-week-old maleC57BL/6 mice (n=8/group) were gavaged daily for 7 days. Blood wascollected from the animals prior to gavage treatment (T=0) and one hourafter gavage at the 7th day of administration (T=7). Center lines showthe median values. Box limits indicate the 25th and 75th percentiles asdetermined by R software. Whiskers extend 1.5 times the interquartilerange from the 25th and 75th percentiles.

FIG. 6 shows counts of bacteria detected in blood from the same micedescribed above for FIG. 5.

FIG. 7 shows jejunal expression of mIL-22 target genes reg3-beta (reg3B)and reg3-gamma (reg3G) in the same mice described above for FIG. 5.After 7 days gavage, animals were sacrificed, and part of the smallintestine (jejunum) was subjected to total RNA isolation followed bycDNA synthesis and real-time PCR. Fold changes and significance arereported based on comparison to the untreated group, and data isnormalized against the housekeeping gene β-actin. Data were analyzedwith the REST software package (Pfaffl et al. 2002). Data are presentedin a box-whisker plot (see comments above with respect to FIG. 5 fordetails).

FIG. 8 shows liver expression of lipopolysaccharide-binding protein(LBP) in the same mice described above for FIG. 5.

FIGS. 9A-9C show results from length measurements in animals after eightweeks of high-fat diet feeding (T0) and after seven subsequent weeks oftreatment (T7) of daily sham gavage of PBS without bacteria (sham),daily gavage of L. reuteri VPL1014 (LR), or daily gavage of theIL-22-secreting L. reuteri VPL3461 (LR-IL22). FIG. 9A shows lengthmeasurements at T0. FIG. 9B shows growth at T7. FIG. 9C shows lengthmeasurements of live versus dead animals.

FIG. 10 shows growth hormone levels in the serum of the mice describedabove for FIGS. 9A-9C at T7.

FIGS. 11A and 11B show percentage differences in body mass index (BMI)in the mice described above for FIGS. 9A-9C. FIG. 11A shows differencesin BMI over the course of seven weeks of treatment (T7-T0). FIG. 11Bshows differences in BMI over the course of six weeks of treatment(T7-T1, wherein T1 refers to the time after one week of treatment).

FIGS. 12A and 12B show absolute liver weights and liver weights relativeto mouse body weights in the mice described above for FIGS. 9A-9C at T7.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides microorganisms such as bacteria that are capableof introducing polypeptides in the bloodstream of a subject. Theinvention provides microorganisms such as bacteria that are morespecifically capable of introducing the polypeptide in the bloodstreamof the subject without the microorganism itself being substantiallyintroduced in the bloodstream of the subject. The invention alsoprovides microorganisms such as bacteria that are capable of introducingthe polypeptide systemically in the subject without the microorganismitself being substantially introduced systemically in the subject.“Introduce” and its grammatical equivalents refer to delivery to a sitein the body. The introducing may result in detectable presence at thatsite. “Systemically introduce” and its grammatical equivalents refer todelivery to the bloodstream or sites in the body via the bloodstream.The systemic introducing may result in detectable presence in thebloodstream or such sites. The sites in which the polypeptides aresystemically introduced include sites or tissues perfused with thebloodstream and which are permeable to polypeptides. The sites in whichthe polypeptides are systemically introduced include sites or tissuesother than those in the gastrointestinal tract. Exemplary sites ortissues include the liver, muscles, lungs, kidneys, pancreas, adiposetissue, or any other site or tissue in the body.

The bacteria of the invention include certain commensal or probioticbacteria. The bacteria may include non-pathogenic, Gram-positivebacteria capable of anaerobic growth. The bacteria are preferably viablein the gastrointestinal tract of mammals. The bacteria may be foodgrade.

Exemplary bacteria include species of lactic acid bacteria (i.e.,species of the order Lactobacillales). The bacteria may include speciesof lactic acid bacteria other than species of the Lactococcus genus. Thebacteria may include species other than species of the Bifidobacteriumgenus

Exemplary bacteria more preferably include species of the Lactobacillusgenus. Exemplary species from the Lactobacillus genus include L.acetototerans, L. acidifarinae, L. acidipiscis, L. acidophilus, L.agilis, L. algidus, L. atimentarius, L. amytolyticus, L. amylophilus, L.amylotrophicus, L. amylovorus, L. animatis, L. antri, L. apodemi, L.aviarius, L. bifermentans, L. brevis, L. buchneri, L. camelliae, L.casei, L. catenaformis, L. ceti, L. coleohominis, L. collinoides, L.composti, L. concavus, L. coryniformis, L. crispatus, L. crustorum, L.curvatus, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp.butgaricus, L. delbrueckii subsp. lactis, L. dextrinicus, L.diolivorans, L. equi, L. equigenerosi, L. farraginis, L. farciminis, L.fermentum, L. fornicalis, L. fructivorans, L. frumenti, L. fuchuensis,L. gallinarum, L. gasseri, L. gastricus, L. ghanensis, L. graminis, L.hammesii, L. hamsteri, L. harbinensis, L. hayakitensis, L. helveticus,L. hitgardii, L. homohiochii, L. iners, L. ingluviei, L. intestinalis,L. jensenii, L. johnsonii, L. katixensis, L. kefiranofaciens, L. kefiri,L. kimchii, L. kitasatonis, L. kunkeei, L. leichmannii, L. lindneri, L.malefermentans, L. coati, L. manihotivorans, L. mindensis, L. mucosae,L. murinus, L. nagelii, L. namurensis, L. nantensis, L. oligofermentans,L. oris, L. panis, L. pantheris, L. parabrevis, L. parabuchneri, L.paracollinoides, L. parafarraginis, L. parakefiri, L. paratimentarius,L. paraplantarum, L. pentosus, L. perolens, L. plantarum, L. pontis, L.psittaci, L. rennini, L. reuteri, L. rhamnosus, L. rimae, L. rogosae, L.rossiae, L. ruminis, L. saerimneri, L. sakei, L. salivarius, L.sanfranciscensis, L. satsumensis, L. secaliphilus, L. sharpeae, L.siliginis, L. spicheri, L. suebicus, L. thailandensis, L. ultunensis, L.vaccinostercus, L. vaginalis, L. versmoldensis, L. vini, L. vitulinus,L. zeae, and L. zymae.

A particularly preferred bacterium is L. reuteri.

A bacterium that can bind mucus in the gastrointestinal tract ispreferred but not required. We surmise that binding mucus in thegastrointestinal tract may place the bacterium in close proximity toepithelial cells. Release of polypeptides so close to the epithelialcells may help systemic delivery of the polypeptides. A bacteriumcapable of binding mucus is L. reuteri, such as L. reuteri VPL1014,discussed below in the examples. The ability to bind mucus can bemediated by the presence of a mucus-binding protein, such as thecell-mucus binding protein CmbA (Jensen et al. 2014).

The bacterium preferably has a low mutation rate. The bacteriumpreferably has a mutation rate of less than about 100×10⁻¹⁰ mutationsper cell per generation, less than about 60×10⁻¹⁰ mutations per cell pergeneration, and more preferably less than about 20×10⁻¹⁰ mutations percell per generation.

The bacterium may be engineered to express a polypeptide of interest.The bacterium accordingly may comprise a recombinant gene configured toexpress the polypeptide of interest. The bacterium may alternatively oradditionally comprise a recombinant DNA sequence that results inincreased expression of the polypeptide of interest. “Recombinant” usedin reference to a gene refers herein to a sequence of nucleic acids thatare not naturally occurring in the genome of the bacterium. Thenon-naturally occurring sequence may include a recombination,substitution, deletion, or addition of one or more bases with respect tothe nucleic acid sequence originally present in the natural genome ofthe bacterium. “Gene” refers to the collection of genetic elementsinvolved in expressing a coding sequence and may include, in addition tothe coding sequence, a promoter, a ribosomal binding site, an enhancer,etc. In some versions, increased expression of the polypeptide ofinterest can result from introducing or modifying (e.g., recombining,substituting, deleting, etc.) genes or other genetic elementsresponsible for regulating expression of the polypeptide of interest,such as genes for transcription factors or signaling factors.

The bacterium may be engineered to produce and release the polypeptide.As used herein, “release” used with respect to the bacterium releasingthe polypeptide refers to disposing the polypeptide outside thebacterium, i.e., in the extracellular environment of the microorganism.Release may occur through secretion of the polypeptide or through lysisof the bacterium, among other possible mechanisms. Elements forengineering a bacterium to secrete a polypeptide are well known in theart. Typical elements include a signal peptide-encoding sequence placedupstream of—and in-frame with—the coding sequence of the polypeptide tobe secreted. The sequences of a large number of signal peptides forbacteria are known in the art. Exemplary signal peptide sequences areavailable at www.cbs.dtu.dk/services/SignalP/. Elements for inducing abacterium to lyse include lytic proteins, which can be expressed from abacterium through recombinant engineering. As used herein, “lyticprotein” refers to any protein that causes or aids in the lysis of amicroorganism.

Lytic proteins are well known in the art. A number of lytic proteins,for example, are found in bacteriophages and serve to lysemicroorganisms during the lytic stages of the bacteriophage's lifecycle. These include holins and lysins (Sheehan et al. 1999). Duringbacteriophage replication, biologically active lysins are present in thecytosol but require expression of a membrane protein, holin, to releasethe virions from the cell. When holin levels are optimal, the lysin canaccess the peptidoglycan layer for cleavage which leads to bacterialcell lysis (Wang et al. 2000). So far, five main groups of lysins havebeen identified that can be distinguished from one and another based onthe cleavage specificity of the different bonds within the peptidoglycan(Fischetti 2009). Structurally, lysins can consist of a single catalyticdomain, which generally is typical for lysins derived frombacteriophages targeting Gram-negative bacteria (Cheng et al. 1994).Bacteriophages targeting Gram-positive bacteria typically encode lysinsthat contain multiple domains: a N-terminal catalytic domain and aC-terminal cell-wall binding domain (Nelson et al. 2006, Navarre et al.1999). A few lysins have been identified that have three domains (Beckeret al. 2009).

A number of other lytic proteins are native to the microorganismsthemselves (Feliza et al. 2012, Jacobs et al. 1994, Jacobs et al. 1995,Lopez et al. 1997). These lytic proteins may affect cell wall metabolismor introduce nicks in the cell wall. Five protein classes aredifferentiated by the wall component they attack (Loessner et al. 2005,Loessner et al. 2002).

In some versions of the invention, the microorganism is configured toconstitutively express a lysin and to express a holin in amaltose-dependent manner. In some versions, the microorganism isconfigured to express both a lysin and a holin in a maltose-dependentmanner.

Lytic proteins can be expressed in a maltose-dependent manner byoperably connecting the coding sequence of the lytic protein to amaltose-sensitive promoter. “Coding sequence” refers to a nucleic acidin a gene that encodes the gene product. “Promoter” refers to anynucleic acid that confers, activates, or enhances expression of anoperably connected coding sequence. “Operably connected” generallyrefers to a connection of two genetic elements in a manner wherein onecan operate on or have effects on the other. “Operably connected” usedin reference to a promoter and a coding sequence refers to a connectionbetween the promoter and the coding sequence such that the codingsequence is under transcriptional control of the promoter. For example,promoters are generally positioned 5′ (upstream) of a coding sequence tobe operably connected to the promoter. In the construction ofheterologous promoter/coding sequence combinations, it is generallypreferred to position the promoter at a distance from the transcriptionstart site that is approximately the same as the distance between thatpromoter and the coding sequence it controls in its natural setting,i.e. in the gene from which the promoter is derived. As is known in theart, some variation in this distance can be accommodated without loss ofpromoter function.

Operably connecting a maltose-inducible promoter to the coding sequenceof a lytic protein induces lysis of the microorganism, release of thelytic protein, and release of any other polypeptides made by themicroorganism, in a maltose-dependent manner. Such release occurs in thegastrointestinal tract due to natural levels of maltose therein.

An exemplary maltose-inducible promoter is represented by SEQ ID NO:1,which is a maltose-inducible promoter found in L. reuteri. Themaltose-inducible promoter represented by SEQ ID NO:1 or variantsthereof are suitable for use in the present invention. Variants of SEQID NO:1 include sequences at least about 80% identical, at least about83% identical, at least about 85% identical, at least about 87%identical, at least about 90% identical, at least about 83% identical,at least about 95% identical, at least about 97% identical, at leastabout 98% identical, or at least about 99% identical to SEQ ID NO:1

Other methods of inducing lysis of bacteria in vivo are known.

The bacteria can be engineered using any methods known in the art.General methods are provided in Green et al. 2012. Methods forengineering lactic acid bacteria such as L. lactis are provided by vanPijkeren et al. 2012, Oh et al. 2014, and Barrangou et al. 2016.

The recombinant gene may be incorporated into the chromosome of thebacterium or may be included on an extra-chromosomal plasmid. Theextra-chromosomal plasmid may replicate at any copy number in the celland, accordingly, be a single-copy plasmid, a low-copy plasmid, or ahigh-copy plasmid. The extra-chromosomal plasmid is preferablysubstantially stable within the bacterium. The rate of loss of theextra-chromosomal plasmid from the bacterium is preferably less thanabout 10% per generation, less than about 5% per generation, or lessthan about 1% per generation, wherein percent per generation refers tothe percent of the population per generation in which the plasmid islost.

The bacterium may be engineered to produce and release any polypeptideof interest. The polypeptide may have any of a number of amino acidchain lengths. In some versions, the polypeptide may have an amino acidchain length of from about 2 to about 4000 amino acids, from about 2 toabout 3000 amino acids, from about 2 to about 2000 amino acids, fromabout 2 to about 1500 amino acids, from about 2 to about 1000 aminoacids, from about 2 to about 500 amino acids, from about 3 to about 250amino acids, or from about 3 to about 225 amino acids. The polypeptidemay have a net positive charge at neutral pH, a net negative charge atneutral pH, or a net neutral charge at neutral pH. The polypeptide ispreferably soluble in water. The polypeptide may form a globular orfibrous structure or may have an intrinsically disordered structure.

The polypeptide may have any of a number of functionalities. Thepolypeptide, for example, may be enzymatic or non-enzymatic. Thepolypeptide may be fluorescent or non-fluorescent. Within thephysiological context of a mammal, the polypeptide may be a cytokine, ahormone, an antibody, an antimicrobial peptide, and an antigenicpeptide, among others.

Exemplary classes of cytokines include interleukins, lymphokines,monokines, interferons (IFNs), colony stimulating factors (CSFs), amongothers. Specific exemplary cytokines include IL-1 alpha (IL1a), IL-1beta (IL1b), IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19, IL-20,IL-21, IL-22, IL-23, IL-24, IL-25, IL-26, IL-27, IL-28, IL-29, IL-30,IL-31, IL-32, IL-33, IL-35, IL-36, IFN-alpha, IFN-beta IFN-gamma,TNF-alpha, TNF-beta, CNTF (C-NTF), LIF, OSM (oncostatin-M), EPO(erythropoietin), G-CSF (GCSF), GM-CSF (GMCSF), M-CSF (MCSF), SCF, GH(growth hormone), PRL (prolactin), aFGF (FGF-acidic), bFGF (FGF-basic),INT-2, KGF (FGF7). EGF, TGF-alpha, TGF-beta, PDGF, betacellulin (BTC),SCDGF, amphiregulin, and HB-EG, among others.

Exemplary hormones include epinephrine, melatonin, triiodothyronine,thyroxine, amylin (or islet amyloid polypeptide), adiponectin,adrenocorticotropic hormone (or corticotropin), angiotensinogen,angiotensin, antidiuretic hormone (or vasopres sin, argininevasopressin), atrial-natriuretic peptide (or atriopeptin), brainnatriuretic peptide, calcitonin, cholecystokinin,corticotropin-releasing hormone, cortistatin, encephalin, endothelin,erythropoietin, follicle-stimulating hormone, galanin, gastricinhibitory polypeptide, gastrin, ghrelin, glucagon, glucagon-likepeptide-1, gonadotropin-releasing hormone, growth hormone-releasinghormone, hepcidin, human chorionic gonadotropin, human placentallactogen, growth hormone, inhibin, insulin, insulin-like growth factor(or somatomedin), leptin, lipotropin, luteinizing hormone, melanocytestimulating hormone, motilin, orexin, oxytocin, pancreatic polypeptide,parathyroid hormone, pituitary adenylate cyclase-activating peptide,prolactin, prolactin releasing hormone, relaxin, renin, secretin,somatostatin, thrombopoietin, thyroid-stimulating hormone (orthyrotropin), thyrotropin-releasing hormone, and vasoactive intestinalpeptide, among others.

Other physiologically active peptides include glucagon-like peptide-1(GLP-1); tachykinin peptides, such as substance P, kassinin, neurokininA, eledoisin, and neurokinin B; peptide PHI 27 (peptide histidineisoleucine 27); pancreatic polypeptide-related peptides, such as NPY(neuropeptide Y), PYY (peptide YY), and APP (avian pancreaticpolypeptide); opioid peptides, such as proopiomelanocortin (POMC)peptides and prodynorphin peptides; AGG01; B-type natriuretic peptide(BNP); lactotripeptides; and peptides that inhibit PCSK9 (Zhang et al.2014).

Exemplary antibodies include single-chain antibodies, single-domainantibodies (sdAbs), and single-chain variable fragments (scFvs).

Exemplary antimicrobial peptides include cathelicidins, defensins,protegrins, mastoparan, poneratoxin, cecropin, moricin, melittin,magainin, dermaseptin, and others.

In preferred versions, the polypeptide that is systemically introducedis a polypeptide capable of treating a condition in a subject with itssystemic introduction. In some versions, The polypeptide that issystemically introduced is a polypeptide capable of treating a conditionin a subject with its systemic introduction but is not capable oftreating a condition in the subject with its local introduction to thegastrointestinal tract alone. The condition may be any conditiondescribed herein.

The inventors have unexpectedly found that administering L. reuteri tothe gastrointestinal tract is capable of delivering producedpolypeptides to the bloodstream without the bacteria themselves beingintroduced in the bloodstream. Accordingly, an aspect of the inventionincludes administering an amount of a bacterium of the invention intothe gastrointestinal tract of a subject. The bacterium may beadministered in any amount effective to introduce the polypeptide in thebloodstream of the subject. Exemplary amounts include from about 1×10³to about 1×10¹⁵, from about 1×10⁵ to about 1×10¹³, from about 1×10⁷ toabout 1×10¹¹, or about 1×10⁹ colony forming units (CFU). Amounts aboveand below these ranges may be acceptable.

The bacterium can be administered to the gastrointestinal tract by anymethod known in the art. The bacterium may be administered orally,rectally, or directly into the gastrointestinal tract via a stoma. Thebacterium is preferably administered directly into or upstream of thesmall intestines, so that the bacterium ultimately passes through orinto the small intestines. The bacterium may be swallowed or introducedvia a tube.

The bacterium may be combined in a composition with a pharmaceuticallyacceptable excipient, carrier, buffer, stabilizer or other material wellknown to those skilled in the art. Such materials should be non-toxicand should not interfere with the efficacy of the bacterium. The precisenature of the carrier or other material may depend on the route ofadministration. The composition may be liquid, solid, or semi-solid. Thecomposition may comprise a foodstuff or may take the form of apharmaceutical composition. Those of relevant skill in the art are wellable to prepare suitable compositions.

The subject to which the bacterium is administered may be an animal,such as a mammal or, more specifically, a human.

In some versions of the invention, the bacterium is administered in anamount effective to introduce the polypeptide in the bloodstream in anamount effective to induce at least one systemic effect in the subject,such as at least one effect in a non-gastrointestinal tissue in thesubject. As used herein, “systemic effect” refers to an effect thatoccurs at a site or tissue in the body other than where the polypeptideis initially released from the bacterium. In the present case, the termrefers to an effect that occurs at a site or tissue other than thegastro-intestinal tract, such as the liver, muscles, lungs, kidneys,pancreas, adipose tissue, or others. The systemic effect preferablyoccurs by virtue of the polypeptide being systemically introduced andaccessing a site or tissue other than gastrointestinal tissue viabloodstream, such that the effect is a direct effect of the polypeptideand is not a secondary effect of a primary effect of the polypeptide inthe gastrointestinal tissue. Such effects are referred to herein as“direct systemic effects.” Direct systemic effects of the systemicallyintroduced polypeptide can be distinguished from secondary effects, forexample, by comparing effects resulting from administering thepolypeptide-producing bacterium into the gastrointestinal tract witheffects resulting from systemically administering the polypeptidedirectly into the bloodstream and effects resulting from locallyadministering the polypeptide directly into the gastrointestinal tract.Direct systemic effects are those that are mirrored by the systemicadministration of the polypeptide into the bloodstream but not the localadministration of the polypeptide into the gastrointestinal tract. Thepresence of direct systemic effects of the polypeptide resulting fromadministering the polypeptide-producing bacterium into thegastrointestinal tract can be an indicator of the polypeptide enteringthe bloodstream, whether or not the polypeptide itself is detected inthe bloodstream.

In some versions, the bacterium is administered to a subject thatsuffers from a condition treatable with systemic introduction of thepolypeptide. In yet other versions, the bacterium is administered to asubject that suffers from a condition treatable with systemicintroduction of the polypeptide but is not treatable with only localintroduction of the polypeptide to the gastrointestinal tract. In eithercase, the polypeptide is introduced in the bloodstream of the subject inan amount effective to treat the condition. As used herein, “treat” usedin reference to a condition refers to ameliorating to any extent thecondition itself or any symptom associated therewith.

In some versions, the bacterium is administered to a subject to preventor inhibit the development of any of the conditions or associatedsymptoms described herein. The subject in such a case may show earlysigns of the condition or symptom, have a genotype that predisposes thesubject to develop the condition or symptom, have a behavior orenvironmental situation that predisposes the subject to develop thecondition or symptom, or otherwise be predisposed to develop thecondition or symptom.

A particular aspect of the invention is directed to introducinginterleukin-22 (IL-22) in the bloodstream of a subject by administeringa bacterium comprising a recombinant interleukin-22 (IL-22) gene. TheIL-22 may be introduced in the bloodstream of the subject in an amounteffective to induce at least one IL-22-dependent effect in anon-gastrointestinal tissue in the subject. An exemplary IL-22 that canbe systemically introduced comprises a sequence of SEQ ID NO:2 or asequence at least about 90%, 95%, 97%, 99% or more identical thereto.

IL-22 is capable of inducing a number of effects in non-gastrointestinaltissues when circulating systemically through the bloodstream. Inrespiratory epithelial cells, for example, IL-22 can increaseantibacterial defense, elevate mucus production, enhance proliferation,and raise production of granulocyte-attracting chemokines. In synovialfibroblasts, IL-22 can elevate RANKL expression and increase productionof monocyte-attracting chemokines. In pancreatic cells, IL-22 canincrease protection against damage, inhibit autophagy, and enhance isletproliferation. In hepatocytes, IL-22 can increase acute-phase proteinproduction, increase protection against damage, and elevate liverprogenitor cell proliferation. In epidermal keratinocytes, IL-22 canincrease antibacterial defense, retard differentiation andcornification, induce production of granulocyte-attracting chemokines,elevate migration and tissue remodeling, and enhance STATS and IL-20expression. See Sabat et al. 2014 and Wang et al. 2014 for additionaldirect IL-22-dependent effects.

Another particular aspect of the invention is directed to introducinginterleukin-22 (IL-22) in the bloodstream of a diabetic subject byadministering a bacterium comprising a recombinant interleukin-22(IL-22) gene. The diabetic subject may suffer from type 1 or type 2diabetes. IL-22 has been shown to have a number of ameliorative effectsin diabetic subjects. In type 2 diabetic subjects, these effects includeameliorating hyperglycemia, insulin resistance, hyperlipidemia, lipiddysregulation in the liver and adipose tissues, endotoxemia, and chronicinflammation. See Wang et al. 2014. As shown in the present examples,IL-22 is also capable of reducing body mass index (BMI).

More generally, subjects in which IL-22 is introduced may include thosesuffering from of insulin resistance, hyperglycemia, lipiddysregulation, hyperlipidemia, obesity, or other manifestations ofmetabolic syndrome. The systemic effect of the systemic introduction ofIL-22 to such subjects may include a reduction in body mass index (BMI),liver weight, liver triglycerides, glucose intolerance, and insulinresistance, or other effects described elsewhere herein.

Another polypeptide that may be introduced in the bloodstream of asubject with the bacteria of the invention is interleukin-35 (IL-35).Systemic administration of IL-35 treats type-1 diabetes and inhibits orslows the development of type-1 diabetes. See Singh et al. 2015. Anexemplary IL-35 that can be systemically introduced is a humanrecombinant IL-35 comprising a sequence of SEQ ID NO:3 or a sequence atleast about 90%, 95%, 97%, 99% or more identical thereto. Bacteria ofthe invention comprising a recombinant IL-35 gene can be administered tosubjects with diabetes, such as type 1 diabetes, to systemicallyintroduce the IL-35 polypeptide in the bloodstream of the subject in anamount effective to treat the diabetes in the subject.

Another polypeptide that may be introduced in the bloodstream of asubject with the bacteria of the invention is insulin. The insulin canbe produced in single-chain form. See, e.g., Rajpal et al. 2009. Anexemplary insulin that can be systemically introduced includes theinsulin A-chain connected to the insulin B-chain by the linker sequenceQRGGGGGQR (SEQ ID NO:4). See Rajpal et al. 2009. Single-chain insulinretains all of the physiological effects of traditional two-chaininsulin, including stimulation of glucose uptake into adipocytes, andsuppression of hepatic gluconeogenesis. Bacteria of the inventioncomprising a recombinant insulin gene can be administered to subjectswith diabetes, insulin resistance, or hyperglycemia to systemicallyintroduce the insulin polypeptide in the bloodstream of the subject inan amount effective to treat the diabetes, or hyperglycemia in thesubject.

Another polypeptide that may be introduced in the bloodstream of asubject with the bacteria of the invention is leptin. Leptin is made byadipose tissue and regulates energy balance by acting on receptors inthe brain. Congenital leptin deficiency (CLD), or generalizedlipodystrophy results in a lack of leptin and can lead to a litany ofdisorders, including morbid obesity (in the case of CLD), diabetes, andinfertility. Systemic leptin replacement therapy mitigates thesedisorders. An exemplary leptin polypeptide that can be systemicallyintroduced includes a polypeptide comprising a sequence of SEQ ID NO:5or a sequence at least about 90%, 95%, 97%, 99% or more identicalthereto. Bacteria of the invention comprising a recombinant leptin genecan be administered to subjects with congenital leptin deficiency orgeneralized lipodystrophy to systemically introduce the leptinpolypeptide in the bloodstream of the subject in an amount effective totreat the obesity, diabetes, infertility or any other aspect of thecongenital leptin deficiency or generalized lipodystrophy.

Another polypeptide that may be introduced in the bloodstream of asubject with the bacteria of the invention is cathelicidin relatedantimicrobial peptide (CRAMP). CRAMP is a small peptide produced bypancreatic islets in response to gut microbiota-derived short-chainfatty acids. Synonyms for CRAMP include CAMP, CAP18, Cnlp, FALL39, andMCL. The islet-derived CRAMP maintains immune homeostasis. CRAMPproduction is defective in non-obese diabetic mice, leading toinflammation and activation of diabetogenic T-cells and resulting intype 1 diabetes (Sun et al. 2015). This process can be reversed bydirect systemic administration of CRAMP. An exemplary CRAMP polypeptidethat can be systemically introduced includes a polypeptide comprising asequence of SEQ ID NO:6 or a sequence at least about 90%, 95%, 97%, 99%or more identical thereto. Bacteria of the invention comprising arecombinant CRAMP gene can be administered to non-obese diabeticsubjects to systemically introduce the CRAMP polypeptide in thebloodstream of the subject in an amount effective to treat the diabetesand/or inflammation in these subjects.

Other polypeptides that may be introduced in the bloodstream of asubject with the bacteria of the invention include peptide inhibitors ofPCSK9. PCSK9 (proprotein convertase subtilisin/kexin type 9) is anegative regulator of the hepatic low density lipoprotein receptor.Inhibition of PCSK9 results in LDL cholesterol-lowering effects. Anumber of peptide inhibitors of PCSK9 are known in the art. See Zhang etal. 2014. Any of these polypeptides or others can be introduced in thebloodstream of a subject with the bacteria of the invention. Aparticularly preferred peptide inhibitor of PCSK9 is referred to as“Pep2-8,” which comprises a sequence of SEQ ID NO:7. Bacteria of theinvention comprising a recombinant gene configured to express one ormore peptide inhibitors of PCKS9 can be administered to subjects withhypercholesterolemia to systemically introduce the peptide inhibitor ofPCSK9 in the bloodstream of the subject in an amount effective to treatthe hypercholesterolemia.

Other polypeptides that may be introduced in the bloodstream of asubject with the bacteria of the invention include lysins, such asbacteriophage-derived lysins (endolysins), i.e. enzybiotics. One of thelargest concerns in 21st century medicine is the development ofmicrobial antibiotic-resistance. Little progress has been made in thediscovery and development of novel antibiotics, andbacteriophage-derived lysins (enzybiotics) constitute promisingalternatives to antibiotics. The enzybiotics interfere withpeptidoglycan cell wall synthesis, mainly of Gram positive bacteria, butdo so in a species specific manner. Exemplary lysins that can besystemically introduced include those described in the references citedherein, all of which are incorporated herein by reference. Bacteria ofthe invention comprising a recombinant gene configured to express one ormore lysins can be administered to subjects with sepsis or infectionwith pathogens such as S. aureus to systemically introduce the lysin inthe bloodstream of the subject in an amount effective to treat thesepsis or infection.

The elements and method steps described herein can be used in anycombination whether explicitly described or not.

All combinations of method steps as used herein can be performed in anyorder, unless otherwise specified or clearly implied to the contrary bythe context in which the referenced combination is made.

As used herein, the singular forms “a,” “an,” and “the” include pluralreferents unless the content clearly dictates otherwise.

Numerical ranges as used herein are intended to include every number andsubset of numbers contained within that range, whether specificallydisclosed or not. Further, these numerical ranges should be construed asproviding support for a claim directed to any number or subset ofnumbers in that range. For example, a disclosure of from 1 to 10 shouldbe construed as supporting a range of from 2 to 8, from 3 to 7, from 5to 6, from 1 to 9, from 3.6 to 4.6, from 3.5 to 9.9, and so forth.

All patents, patent publications, and peer-reviewed publications (i.e.,“references”) cited herein are expressly incorporated by reference tothe same extent as if each individual reference were specifically andindividually indicated as being incorporated by reference. In case ofconflict between the present disclosure and the incorporated references,the present disclosure controls.

It is understood that the invention is not confined to the particularconstruction and arrangement of parts herein illustrated and described,but embraces such modified forms thereof as come within the scope of theclaims.

Examples Bacterial Strains, Plasmids, Media, and Culture.

Bacterial strains and plasmids used in the present examples are listedin Table 1. Lactobacillus reuteri VPL1014 and its derivatives wereroutinely cultured at 37° C. in deMan Rogosa Sharpe (MRS) medium (Difco,BD Biosciences). Where appropriate, erythromycin was added to a finalconcentration of 5 μg/ml. Competent cells of L. reuteri were prepared asdescribed before (Ahrné et al. 1992). To test IL-22 expression and toprepare bacteria for animal experiments, bacteria were cultured inLactobacilli Defined Medium-III (LDM-III, Table 2).

Specifically, L. reuteri VPL1014 was inoculated in 10 ml MRS broth, andL. reuteri VPL3461 was inoculated in 10 ml MRS containing 5 μm/mlerythromycin at 37° C. Overnight-cultures of each strain weresub-cultured in MRS at OD₆₀₀=0.1. At OD600≥1≤1.2 cells were harvested bycentrifugation (5,000 rpm for 5 min), and the cell pellets were washedtwice with LDM-III. Washed cell pellets, each derived from 10-mlculture, were stored at −80° C. until use. From this step onwards, noantibiotics were supplemented to the culture media. At the day ofgavaging, the cell pellets were resuspended in 10 ml freshly preparedpre-warmed LDM-III and incubated at 37° C. until OD₆₀₀≥3.5≤3.7. Bacteriawere concentrated 10-fold, and suspensions were made containing ˜10¹⁰CFU/ml L. reuteri VPL1014 or VPL3461. For animal experiments (see below)100 μl of the suspension was administrated by oral gavage to thecorresponding animals.

TABLE 1 Bacterial strains and plasmids used in the present examples.Strain or plasmid Characteristics Source L. reuteri A derivative of L.reuteri ATCC PTA 6475, U.S. VPL1014 ATCC PTA 6475, Pat. No. 7,344,867 tohuman breast milk isolate BioGaia AB (Lerum, SE), and van Pijkeren etal. 2012 L. reuteri L. reuteri VPL1014 harboring Described hereinVPL3461 pVPL3461 pJP028 Em^(R), derivative Described herein of pNZ8048containing promoter from L. reuteri SD2112, signal peptide from L.reuteri JCM1112, and LPXTG (cell wall anchor domain) pVPL3461 Em^(R),derivative of pJP028 Described herein omitting LPXTG domain andharboring mIL-22 gene

TABLE 2 Lactobacilli Defined Medium-III (LDM3) composition. Basal MediumAmount Ingredient per Liter K₂HPO₄ 1.50 g KH₂PO₄ 1.50 g Sodium Acetate15.00 g Sodium Citrate, Dihydrate 0.25 g Tryptophan 0.05 g Asparagine,Monohydrate 0.23 g Vitamin-free Casamino acid 10.00 g Cysteine-HCl,Monohydrate 0.22 g Tween80 (10% v/v) 10 ml Dissolve in 937.5 ml of DIwater and autoclave at 121° C. for 15 min. Prepare stock solutions (asbelow) and add to sterile Basal Medium. Vitamin Solution (in 25 ml dH₂O)0.5 ml Thiamin HCl 10 mg ρ-aminobenzonoic acid 2 mg Calcium pantothenicacid 20 mg Niacin 50 mg Pyridoxin HCl 25 mg Biotin Solution (in 50 ml0.01M HCl) 0.5 ml Biotin 4 mg 96% EtOH 40 μL Riboflavin Solution (in 50ml dH₂O) 5 ml Riboflavin 4 mg Folic Acid Solution (in 50 ml 0.001M NaOH)0.5 ml Folic acid 10 mg Nucleic Acid Solution (in 15 ml 1M HCl) 3 mlAdenine hemisulfate 50 mg Guanine 40.3 mg Cytidylic acid 150 mg UracilSolution (in 10 ml 1M NaOH) 1 ml Uracil 200 mg Thymidine Solution (in12.5 ml dH₂O) 1 ml Thymidine 20 mg Salt Solution (in 10 ml dH₂O) 1 mlMgSO₄ 0.793 g MnSO₄ 0.128 g FeSO₄ 0.130 g Glucose (40% w/v) 50 ml Total1 L (LDM), final pH 6.5

Mutation Rate.

A suitable microorganism for delivering peptides preferably has a lowmutation rate. The mutation rate of L. reuteri VPL1014 was compared withthat of a number of other microorganisms using conventional methods(Rosche et al. 2000, Foster et al. 2006). As shown in FIGS. 1A and 1B,L. reuteri displayed an exceptionally low mutation rate, particularlycompared to the other tested probiotic microorganisms.

Reagents and Enzymes.

Cloning was performed via ligation cycle reaction (LCR; Kok et al.2014). Enzymes and reagents for LCR were purchased from Fermentas.Polymerase chain reaction (PCR) for cloning purposes was performed withthe high-fidelity enzyme Phusion Hot Start Polymerase II (Fermentas).PCR for screening purposes was performed with Taq polymerase (DenvilleScientific). To concentrate the LCR reaction prior toelectrotransformation into L. reuteri, we used Pellet PaintCo-Precipitant (Novagen). Oligonucleotides and synthetic double-strandedDNA fragments were purchased from Integrated DNA Technologies. Alloligonucleotides and synthetic DNA fragments used in this study arelisted in Table 3.

TABLE 3 Oligonucleotides and synthetic DNA used in the present examples.Oligo- nucleotides Sequence oVPL329attccttggacttcatttactgggtttaac (SEQ ID NO: 8) oVPL363taatatgagataatgccgactgtac (SEQ ID NO: 9) oVPL1219ttcatggggatgaatgcttctgctaatacattaccagttaatactcgttg (SEQ ID NO: 10)oVPL1220cttggttttctaattttggttcaaagatcaaacacaagcattacgtaaactc (SEQ ID NO: 11)oVPL1221 gcttgaaacgttcaattgaaatggca (SEQ ID NO: 12) oVPL1222tgtaaaaccaataaggactgaagc (SEQ ID NO: 13) oVPL1223ggagttgcttcagtccttattggttttacattcatggggatgaatgcttctgctaataca (SEQID NO: 14) oVPL1224tgatctttgaaccaaaattagaaaaccaaggcttgaaacgttcaattgaaatggcaatta (SEQ IDNO: 15) oVPL1313 actccctgaagaatataccctcc (SEQ ID NO: 16) oVPL1314cgctattgagcacagatacgag (SEQ ID NO: 17) oVPL1315atgcttccccgtataaccatca (SEQ ID NO: 18) oVPL1316ggccatatctgcatcataccag (SEQ ID NO: 19) oVPL1321gatcaccgacaagggcctg (SEQ ID NO: 20) oVPL1322ggctatgaaactcgtactgcc (SEQ ID NO: 21) oVPL1325ggctgtattcccctccatcg (SEQ ID NO: 22) oVPL1326ccagttggtaacaatgccatgt (SEQ ID NO:2 3) gVPL1ATTCATGGGGATGAATGCTTCTGCTAATACATTACCAGTTAATACTCGTTGTAAATTAGAAGTTAGTAATTTTCAACAACCATATATTGTTAATCGTACTTTTATGTTAGCTAAAGAAGCTAGTTTAGCTGATAATAATACTGATGTTCGTTTAATTGGTGAAAAATTATTTCGTGGTGTTAGTGCTAAAGATCAATGTTATTTAATGAAACAAGTTTTAAATTTTACTTTAGAAGATGTTTTATTACCACAAAGTGATCGTTTTCAACCATATATGCAAGAAGTTGTTCCATTTTTAACTAAATTAAGTAATCAATTAAGTAGTTGTCATATTAGTGGTGATGATCAAAATATTCAAAAAAATGTTCGTCGTTTAAAAGAAACTGTTAAAAAATTAGGTGAAAGTGGTGAAATTAAAGCTATTGGTGAATTAGATTTATTATTTATGAGTTTACGTAATGCTTGTGTTTGATCTTTGAACCAAAATTAGAAAACCAAGG (SEQ ID NO: 24)Construction of L. reuteri VPL1014 that Secretes mIL-22.

Our aim was to engineer Lactobacillus reuteri VPL1014 to secrete themurine cytokine interleukin-22 (mIL-22). We first opted for expressionfrom the multicopy plasmid pJP028 to maximize mIL-22 production. pJP028is a derivative of pNZ8048 (de Ruyter et al. 1996) in which thenisin-expression cassette was replaced with a secretion cassette. By PCR(oVPL1221-oVPL1222), we amplified the backbone of pJP028, omitting thecell wall anchor domain, to yield a 4.579 kb product. For optimalexpression of mIL-22 in our expression host, L. reuteri, we firstapplied in-silico codon optimization of the mIL-22 coding sequence usingthe online software, OPTIMIZER (genomes.urv.es/OPTIMIZER/, Table 4)followed by synthesis. The resulting synthetic product (gVPL1) wasamplified by PCR (oVPL1219 and oVPL1220), followed LCR (Kok et al. 2014)placing the gVPL1 fragment between the start and stop codon located onthe pJP028 backbone. The LCR mixture was precipitated and transformed inL. reuteri VPL1014. Transformants were screened by PCR (oVPL329-oVPL363)to confirm cloning of mIL-22. One positive clone was colony purified, a1.584 kb amplicon was generated by colony PCR, and the integrity of theconstruct was confirmed by DNA sequencing (GeneWiz). The resultantstrain was named VPL3461. We hereafter refer to pVPL3461 when itconcerns the plasmid that encodes codon-optimized mIL-22 (FIG. 2).

The nucleotide sequence of pVPL3461 is represented by SEQ ID NO:25. Thenucleotide sequence of the IL-22 promoter (L. reuteri native promoter)in pVPL3461 is represented by SEQ ID NO: 26. The nucleotide sequenceencoding the signal peptide (SP) in pVPL3461 is represented by SEQ IDNO:27. The nucleotide sequence encoding IL-22 in pVPL3461 is representedby SEQ ID NO:28. The nucleotide sequence of the inverted repeat (IR) inpVPL3461 is represented by SEQ ID NO:29. The nucleotide sequence of thechloramphenicol marker (Cm) in pVPL3461 is represented by SEQ ID NO:30.The nucleotide sequence of the Phelp promoter in pVPL3461 is representedby SEQ ID NO:31. The nucleotide sequence of the erythromycin marker (Em)in pVPL3461 is represented by SEQ ID NO:32.

Additionally, a construct from the pVPL3461 plasmid comprising thepromoter, signal peptide, and mIL-22 coding sequence was excised frompVPL3461 and incorporated in the L. reuteri chromosome using methodsknown in the art. The resultant strain was named VPL3461chr.

TABLE 4 Codon optimization table for L. reuteri F275.*^(#) Fields:[sequence of nucleotide triplet] [frequency: per thousand] ([number])UUU 29.5 (16802) UCU 9.7 (5521) UAU 24.8 (14106) UGU 4.4 (2479) UUC 11.3(6447) UCC 4.0 (2249) UAC 12.4 (7068) UGC 1.5 (861) UUA 36.4 (20706) UCA15.0 (8537) UAA 2.3 (1307) UGA 0.4 (219) UUG 15.4 (8765) UCG 4.3 (2458)UAG 0.7 (374) UGG 10.8 (6134) CUU 22.1 (12555) CCU 9.7 (5489) CAU 15.3(8708) CGU 14.1 (7995) CUC 6.3 (3597) CCC 3.4 (1927) CAC 8.0 (4562) CGC5.9 (3360) CUA 9.4 (5359) CCA 17.7 (10090) CAA 35.0 (19877) CGA 8.6(4869) CUG 5.3 (3005) CCG 6.0 (3428) CAG 11.7 (6653) CGG 9.9 (5610) AUU50.7 (28857) ACU 22.3 (12657) AAU 36.1 (20541) AGU 15.6 (8850) AUC 16.7(9524) ACC 9.8 (5550) AAC 15.8 (8968) AGC 6.7 (3786) AUA 5.8 (3300) ACA16.6 (9464) AAA 36.6 (20829) AGA 3.3 (1872) AUG 26.9 (15321) ACG 9.2(5230) AAG 30.3 (17232) AGG 1.4 (792) GUU 35.0 (19884) GCU 29.0 (16508)GAU 43.5 (24740) GGU 24.3 (13830) GUC 9.2 (5210) GCC 12.4 (7053) GAC15.2 (8617) GGC 10.9 (6178) GUA 16.1 (9176) GCA 25.3 (14409) GAA 45.6(25918) GGA 19.8 (11244) GUG 7.7 (4354) GCG 9.8 (5573) GAG 11.2 (6360)GGG 10.1 (5771) *This table was made based on 568,715 codons among 1,900CDSs on chromosomal DNA of strain F275. ^(#)Coding GC 39.50% 1st letterGC 51.33% 2nd letter GC 35.17% 3rd letter GC 32.00%.Determine mIL-22 Secretion.

Strains L. reuteri VPL1014 and VPL3461 were cultured in LDM-III asdescribed above, and the supernatants were collected aftercentrifugation (5 min at 3,214×g), followed by filter-sterilization(0.22 μm, Millipore). One hundred microliters of filter-sterilizedsupernatant from L. reuteri VPL1014 and VPL3461 was assessed for thepresence of mIL-22 by ELISA (R&D systems). Production of mIL-22 couldnot be detected for L. reuteri 6575-VPL (15 pg/ml cut-off limit), whilestrain VPL3461 secreted mIL-22 at levels of 164.2±13.1 ng/ml (n=3). SeeFIG. 3A.

Secretion of mIL-22 from VPL3461chr was similarly tested. VPL3461chrshowed detectable mIL-22 secretion. See FIG. 3B.

Plasmid Stability of pVPL3461 in L. reuteri VPL1014.

Prior to assessing biological activity of the L. reuteri-produced mIL-22in mice, we first assessed the stability of pVPL3461. Normally,selection of plasmids is achieved by supplementation of an antibiotic,but we wanted to avoid the supplementation of antibiotics in mice tomaintain a fully competent microbiota. VPL3461 was cultured overnight inLDM-III (supplemented with antibiotics). Cells were washed to removeresidual antibiotics, followed by sub-culturing to antibiotic-freeLDM-III (OD600=0.1). After 1 passage (20 hr, ˜10 generations), we showedthat 96% of the cell population was resistant to erythromycin,demonstrating that the rate of loss of pVPL3461 was 0.4% per generation,and would be considered stable enough for in-vivo assessment ofbiological activity.

Animal Trial.

Twenty-four 6-week old male B6 mice (C57BL/6J) were purchased fromJackson Labs (Bar Harbor, Me.). Animals were housed at anenvironment-controlled facility with a 12-hour light and dark cycle.Both diet (standard chow, LabDiet, St Louis, Mo.) and water were freelyavailable to the animals. After transport, animals were allowed toadjust to the new environment for two weeks, after which treatment bygavage started. Three groups of 8 animals per group were treated dailyfor 7 consecutive days. Treatments were sham gavage where the animalswere subjected to insertion of a gavaging needle without administeringanything (control), gavage of L. reuteri VPL1014 (WT group) and gavageof L. reuteri VPL3461 (LR_mIL-22). Bacterial load administrated was˜1×10⁹ CFU in a volume of 100 μl of the respective bacterialsupernatant. See FIG. 4.

Blood Collection to Assess Plasma IL-22 Levels.

At T=0 (prior to the start of treatment) and at T=7 (2 hours after thelast gavage) of the animal trial, blood was collected (50 μl per animal)via retro orbital puncture. Plasma was isolated from whole blood sampleby centrifugation at 9,000 rpm for 7 min and the plasma fraction wasstored at −80° C. until use. By ELISA (as described above) we determinedplasma mIL-22 levels. See FIG. 4.

Plasma IL-22 levels after 7 days gavage are shown in FIG. 5. The miceadministered L. reuteri VPL3461 showed a statistically significantincrease in plasma IL-22 levels compared to controls.

We also assessed whether the administered L. reuteri VPL1014 and L.reuteri VPL3461 could be detected in the bloodstream of the animalsafter 7 days gavage. From each animal, 50 μl blood was plated on deManRogosa Sharp (MRS) medium that is selective for a broad range of lacticacid bacteria, including L. reuteri. The results are shown in FIG. 6.The prolonged daily administration of L. reuteri did not increase thetotal number of lactic acid bacteria in the bloodstream. As determinedby colony morphology, the bacteria detected in the bloodstream ofanimals that were gavaged with L. reuteri were not L. reuteri. L.reuteri yields (after 48 h) on MRS plates small-medium sized coloniesthat are opaque. From the 3 animals in which we detected bacteria in thebloodstream, all colonies were pigmented, mostly yellow, and some werered-ish. Some colonies were also extremely large. The size combined withthe pigmented phenotype made it evident that the recovered bacteria inthe bloodstream were not L. reuteri.

These results indicate that the systemic increase of IL-22 was not aresult of L. reuteri VPL3461 itself entering the bloodstream.

cDNA Synthesis.

To assess biological functionality of L. reuteri secreted mIL-22, weassess gene expression levels of reg3-beta and reg3-gamma. Both genesare known to be upregulated by IL-22 (Loonen et al. 2013, Sovran et al.2015). Part of the small intestine (jejunum) of each animal wasprocessed for RNA isolation. First, samples were homogenized (Omni TH,Omni International) followed by RNA isolation and on-column DNaseItreatment (Qiagen), after which an additional DNase treatment wasconducted (RQI DNase; Promega, Madison, Wis.). RNA was quantified byQubit analysis (Invitrogen). One μg RNA was reverse transcribed usingthe iScript cDNA synthesis kit (Bio-Rad Laboratories, Richmond, Calif.).See FIG. 4.

Quantitative Real-Time PCR.

Relative gene expression levels were determined using the CFX96™real-time PCR (Bio-Rad). Expression of reg3-beta and reg3-gamma wasdetermined relative to that of the housekeeping gene β-actin. TheqRT-PCR was performed with the SYBR Green PCR master mix (Bio-Rad).Primers for amplification of: reg3b (oVPL1313-oVPL1314), reg3g(oVPL1315-oVPL1316), and β-actin (oVPL1325-oVPL1326) are listed in Table3. Gene expression of the reg genes in the jejunum tissues relative toβ-actin was determined by the Relative Expression Software Tool (REST),which allows comparison of gene expression between groups of animals(Pfaffl et al. 2001 and 2002).

As shown in FIG. 7, mice administered IL-22-expressing L. reuteriVPL3461 showed an average of 4.7-fold and 3-fold increased expression ofreg3-beta and reg3-gamma, respectively in the jejunum compared to miceadministered wild-type L. reuteri, demonstrating that the secreted IL-22is biologically active.

We also determined liver expression of the gene encoding thelipopolysaccharide-binding protein (LBP), which is known to be regulatedby IL-22. Expression levels were relative to that of the control(β-actin). As shown in FIG. 8, liver LBP expression was not changed inanimals that received wild-type L. reuteri. Animals administered theIL-22-expressing L. reuteri VPL3461 displayed an increased level of LBPgene expression, varying from 1.5-fold to 3.5-fold. We did not detect astatistical difference in gene expression, but we predict including moreanimals per group will show a statistical difference.

Metabolic Syndrome Trial.

IL-22 has been shown to alleviate metabolic disorders and provide othertherapeutic effects in diabetic subjects. See Wang et al. 2014. Wetested whether administering IL-22-secreting L. reuteri to mice withdiet-induced obesity could recapitulate these effects.

Thirty-six 6-week old male B6 mice (C57BL/6J) were purchased fromJackson Labs (Bar Harbor, Me.). Animals were housed at an environmentalcontrolled facility with a 12-hour light and dark cycle. Aftertransport, animals were caged (4 mice per cage) and immediately placedon an ad libitum high-fat diet: 45% kcal fat diet containing 21% milkfat and 2% soybean oil (Cat. No. TD08811, Envigo, Indianapolis, Ind.),for eight weeks. Based on prior work, animals placed on this diet foreight weeks develop signs of metabolic syndrome, including glucoseintolerance and insulin sensitivity.

After eight weeks on the high-fat diet, we initiated the treatment ofdaily gavage for a period of seven weeks. Animals in a first group (12animals) received a sham gavage of 100 μl PBS without bacteria. Animalsin a second group (12 animals) received 100 μl of L. reuteri VPL1014(10⁹ CFU). Animals in a third group (12 animals) received 100 μl of theIL-22-secreting L. reuteri VPL3461 (10⁹ CFU).

The length (nose to anus) of the animals was determined after eightweeks high-fat diet feeding (T0), and was subsequently determined everyweek after for seven weeks (T7). Each animal was measured three timesand the values were averaged. After eight weeks high-fat diet feedingbut prior to the start of the treatment (T0) we observed that theanimals assigned to be receiving treatment were similar in length(P=0.88) but both groups were marginally smaller than the control group(control vs WT, P=0.09; control vs recombinant, P=0.04). See FIG. 9A.After seven weeks of treatment (T7) we observed that the animals gavagedwith the IL-22-secreting L. reuteri grew faster than animals gavagedwith L. reuteri wild-type (P<0.0001) or PBS control (P<0.0001). See FIG.9B. The increased growth is purely driven by recombinant IL-22 that isdelivered by L. reuteri because L. reuteri wild-type does not influencegrowth compared to the PBS control (P=0.66)

Healthy mice have a natural curve in their spine. When mice are obese,the excess weight will press the spine down. When measuring length ofthe animal from nose to anus, obese mice may be perceived to be longer.To determine if this would have affected our body length data, wemeasured animals alive and after euthanasia at T7. When anesthetized ordead, any bias derived from differences in curvature will be lost as theanimal is completely relaxed. As shown in FIG. 9C, there is nodifference in the body length of the animals when measured alive ordead. This finding conclusively confirmed that recombinant L. reuterisecreting IL-22 promotes growth.

Our growth data led us to measure growth hormone levels in the serum. Asshown in FIG. 10, mice treated with IL-22-secreting L. reuteri hadincreased levels of growth hormone compared to the PBS control (P=0.03)at T7. Levels were also higher in the recombinant group compared to thewild-type but this was not statistically significant (P=0.09).

In mice, the body mass index (BMI) can be an indication of metabolicsyndrome. We determined the BMI of the mice as follows: (body weight(g)/[nose-anus length (mm)]²). As shown in FIGS. 11A and 11B, L.reuteri-derived IL-22 reduces the change in BMI over the course of sevenweeks (T7-T0) and six weeks (T7-T1), respectively.

Following seven weeks treatment (T7), animals were killed, tissues wereharvested, and liver weights were determined. Liver weights are shown asabsolute liver weights (FIG. 12A) or liver weight relative to mouse bodyweight (FIG. 12B). Both metrics showed that IL-22-secreting L. reuteriyielded significantly lower liver weights compared to the wild-type L.reuteri or PBS control.

These results show that oral administration of recombinant L. reuteriengineered to secrete IL-22 systemically delivers IL-22 in a manner thatresults in systemic physiological effects. In the present case, thesystemic physiological effects included an increase in growth, anincrease in growth hormone in the plasma, a reduction in BMI, and areduction in liver weight. The administration reversed many effectsassociated with metabolic syndrome. We predict that systemic delivery ofIL-22 will also reverse many metabolic symptoms of diabetic subjects,including hyperglycemia and insulin resistance, and will improve insulinsensitivity, preserve gut mucosal barrier and endocrine functions,decrease endotoxemia and chronic inflammation, and reverse thedysregulation of lipid metabolism in liver and adipose tissues.

Delivery of Peptides Other than IL-22.

L. reuteri can be used to systemically deliver polypeptides other thanIL-22. This can be performed by replacing the mIL-22 reading frame fromthe pVPL3461 plasmid and replacing it with the reading frame of anypolypeptide of interest. The edited plasmid can then be introduced intoL. reuteri using methods described above, and the L. reuteri harboringthe edited plasmid can be administered as described above. We predictthat the L. reuteri so modified will be capable of systemicallydelivering any polypeptide of interest without the bacterium itselfbeing distributed systemically. We predict that diseases and conditionsthat are alleviated by systemic administration of such polypeptides willbe alleviated with the L. reuteri-dependent systemic delivery of thepeptides.

Statistical Analysis.

In the present examples, ANOVA (analysis of variance) was used for dataanalysis, and significance in comparisons between groups was analyzed byt-test. Significant difference was considered when P-value is lower than0.05.

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1-20. (canceled)
 21. A method of systemically introducing a polypeptideinto a bloodstream of a subject, the method comprising administeringinto the gastrointestinal tract of the subject a bacterium that producesand releases the polypeptide, wherein the bacterium comprises arecombinant gene configured to express the polypeptide, wherein thebacterium is administered in an amount effective to introduce thepolypeptide in the bloodstream of the subject in a detectable amountwithout the bacterium being introduced in the bloodstream of the subjectin a detectable amount.
 22. The method of claim 21, wherein thebacterium is administered in an amount effective to introduce thepolypeptide in the bloodstream in an amount effective to induce at leastone direct systemic effect in the subject.
 23. The method of claim 21,wherein the bacterium is administered in an amount effective tointroduce the polypeptide in the bloodstream in an amount effective toinduce at least one direct effect in a non-gastrointestinal tissue inthe subject.
 24. The method of claim 21, wherein the bacterium isadministered in an amount effective to introduce the polypeptide in thebloodstream in an amount effective to induce at least one direct effectin a tissue selected from the group consisting of liver, muscles, lungs,kidneys, pancreas, and adipose tissue in the subject.
 25. The method ofclaim 21, wherein the subject suffers from a condition treatable withsystemic introduction of the polypeptide and wherein the polypeptide isintroduced in the bloodstream of the subject in an amount effective totreat the condition.
 26. The method of claim 21, wherein the subjectsuffers from a condition treatable with systemic introduction of thepolypeptide but not treatable with local introduction of the polypeptideto the gastrointestinal tract without systemic introduction of thepolypeptide, and wherein the polypeptide is introduced in thebloodstream of the subject in an amount effective to treat thecondition.
 27. The method of claim 21, wherein the recombinant gene iscodon optimized.
 28. The method of claim 21, wherein the polypeptide isselected from the group consisting of a cytokine, a hormone, anantibody, an antimicrobial peptide, and an antigenic peptide.
 29. Themethod of claim 21, wherein the polypeptide is selected from the groupconsisting of interleukin-22 (IL-22), interleukin-35 (IL-35), insulin,leptin, cathelicidin related antimicrobial peptide, a peptide inhibitorof proprotein convertase subtilisin/kexin type 9 (PCSK9), and anendolysin.
 30. The method of claim 29, wherein the subject suffers fromat least one condition selected from the group consisting of insulinresistance, hyperglycemia, lipid dysregulation, hyperlipidemia, andobesity, and wherein the polypeptide is introduced in the bloodstream ofthe subject in an amount effective to treat the at least one condition.31. The method of claim 21, wherein the polypeptide is interleukin-22(IL-22).
 32. The method of claim 21, wherein the bacterium expresses amucus-binding protein.
 33. The method of claim 21, wherein the bacteriumexpresses CmbA.
 34. The method of claim 21, wherein the bacterium has amutation rate less than about 100×10⁻¹⁰ mutations per cell pergeneration.
 35. The method of claim 21, wherein the bacterium comprisesa member of lactic acid bacteria.
 36. The method of claim 21, whereinthe bacterium comprises a member of lactic acid bacteria other than amember of the Lactococcus genus.
 37. The method of claim 21, wherein thebacterium comprises a member of Lactobacillus.
 38. The method of claim21, wherein the bacterium expresses a mucus-binding protein and has amutation rate less than about 100×10⁻¹⁰ mutations per cell pergeneration.
 39. The method of claim 38, wherein the mucus-bindingprotein is CmbA.
 40. The method of claim 39, wherein the recombinantgene is codon optimized.